isiKnock: in silico knockouts in biochemical pathways

Abstract

SummaryisiKnock is a new software that automatically conducts in silico knockouts for mathematical models of biochemical pathways. The software allows for the prediction of the behavior of biological systems after single or multiple knockout. The implemented algorithm applies transition invariants and the novel concept of Manatee invariants. A knockout matrix visualizes the results. The tool enables the analysis of dependencies, for example, in signal flows from the receptor activation to the cell response at steady state.\n\nAvailability and ImplementationisiKnock is an open-source tool, freely available at http://www.bioinformatik.uni-frankfurt.de/tools/isiKnock/index.php. It requires at least Java 8 and runs under Microsoft Windows, Linux, and Mac OS.\n\nContactina.koch@bioinformatik.uni-frankfurt.de